The memory reconsolidation theory holds that consolidated memories can be reactivated into an unstable state again, which is called the reconsolidation process. During this period, the activated memories are susceptive to new information and therefore, the interruption of it can update or eliminate original memories. Behavioral or pharmacological interventions after memory reactivation are proved to be an effective way to extinguish fear memories and prevent relapse. The behavioral intervention, which is the so-called retrieval-extinction paradigm can eliminate conditioned fear through applying extinction training during the reconsolidation time window. The neural mechanisms of this effect, however, are still largely unknown. Based on reviewing present studies in animals and humans, we concluded the critical brain areas which were proved to be playing an important part in retrieval extinction process and their effect mechanisms, including hippocampus, prefrontal cortex and amygdala. Furthermore, we summarized the controversial points in theories and manipulations in order to provide insights for future explorations.